Hello Justin, Thanks a lot for your reply. I am using the option "freezegrps" in my .mdp file, given below: -----------------------------------------------------------------------------------------------------------------------------------------
;define = -DSTRONG_POSRES define = -DPOSRES ; position restrain the protein ; Run parameters integrator = md ; leap-frog integrator nsteps = 10000 ; 2 * 50000 = 100 ps dt = 0.002 ; 2 fs ; Output control nstxout = 100 ; save coordinates every 0.2 ps nstvout = 100 ; save velocities every 0.2 ps nstenergy = 100 ; save energies every 0.2 ps nstlog = 100 ; update log file every 0.2 ps ; Bond parameters continuation = no ; first dynamics run constraint_algorithm = lincs ; holonomic constraints constraints = all-bonds ; all bonds (even heavy atom-H bonds) constrained lincs_iter = 1 ; accuracy of LINCS lincs_order = 4 ; also related to accuracy ; Neighborsearching ns_type = grid ; search neighboring grid cels nstlist = 5 ; 10 fs rlist = 1.0 ; short-range neighborlist cutoff (in nm) rcoulomb = 1.0 ; short-range electrostatic cutoff (in nm) rvdw = 1.0 ; short-range van der Waals cutoff (in nm) ; Electrostatics coulombtype = PME ; Particle Mesh Ewald for long-range electrostatics pme_order = 4 ; cubic interpolation fourierspacing = 0.16 ; grid spacing for FFT ; Temperature coupling is on tcoupl = V-rescale ; modified Berendsen thermostat tc-grps = Protein Non-Protein ; two coupling groups - more accurate tau_t = 0.1 0.1 ; time constant, in ps ref_t = 300 300 ; reference temperature, one for each group, in K ; Pressure coupling is off pcoupl = no ; no pressure coupling in NVT ; Periodic boundary conditions pbc = xyz ; 3-D PBC ; Dispersion correction DispCorr = EnerPres ; account for cut-off vdW scheme ; Velocity generation gen_vel = yes ; assign velocities from Maxwell distribution gen_temp = 300 ; temperature for Maxwell distribution gen_seed = -1 ; generate a random seed freezegrps = Fixed freezedim = Y Y Y -------------------------------------------------------------------------------------------------------------------------------------------- I was just wondering how to give the "energygrp_excl" parameters with it. Can you please guide me regarding this and also please go through the other parameters in the .mdp file. Regards, Anirban On Wed, Apr 28, 2010 at 4:52 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: > >> Hello Justin, >> >> In my topology file I am declaring: >> >> --------------------------------------------------------------------------------------------------------------- >> ; Include Position restraint file >> #ifdef POSRES >> #include "posre.itp" >> #endif >> >> ; Strong position restraints on rest of B2AR >> #ifdef STRONG_POSRES >> #include "strong_posre.itp" >> #endif >> >> > What is in strong_posre.itp? Presumably you're only restraining certain > residues, right? Did you create this with genrestr and an appropriate index > group? > > > ; Include water topology >> #include "spc.itp" >> >> ----------------------------------------------------------------------------------------------------------------- >> And in my .mdp file I am giving: >> >> ----------------------------------------------------------------------------------------------------------------- >> define = -DSTRONG_POSRES ; Run parameters >> integrator = md ; leap-frog integrator >> nsteps = 5000 ; 2 * 50000 = 100 ps >> dt = 0.002 ; 2 fs >> >> ------------------------------------------------------------------------------------------------------------------- >> > > If this is the entirety of your .mdp file, you're asking for trouble. > Allowing all other parameters to be taken as default is very dangerous, and > probably inappropriate (most notably cutoff electrostatics). > > > But now what I am getting is that if I run MD using these restraints on >> the helical portion of the protein, then I am getting LINCS errors. However, >> if I allow the entire protein to move during MD, then it is running fine. >> What mistake am I making? And how can I freeze properly the helical portions >> and simulate only the loop? Thanks a lot in advance. >> >> > Recognize that there is a difference between "freezing" and "restraining." > Read in the manual about what freezing is versus position restraints. > Either way, you should be able to get things up and running, but position > restraints are a bit easier to implement. > > If an unrestrained simulation runs fine (using that fragmented .mdp file?) > then there are probably just bad clashes in the system that the restraints > are not allowing to relax. > > -Justin > > Regards, >> >> Anirban >> >> >> On Fri, Apr 23, 2010 at 5:37 PM, Justin A. Lemkul <jalem...@vt.edu<mailto: >> jalem...@vt.edu>> wrote: >> >> >> >> Anirban Ghosh wrote: >> >> Hi ALL, >> >> I want to do a MD simulation by restraining (freezing) the >> helical portions and allowing only the loop regions to move. I >> tried doing this by applying heavy restrain on the helical >> residues by generating a .itp file with the "genrestr" command >> with an index file containing the desired residue numbers. >> However during the simulation I am finding that the entire >> protein is moving. Am I doing anything wrong? Or is there any >> other way to freeze a portion of a protein? Any suggestion is >> welcome. thanks a lot in advance. >> >> >> If your protein is still moving, then you aren't correctly applying >> your position restraints. Without seeing your topology and .mdp >> file, there's no way to know what you're doing wrong. >> >> You can also use the freezegrps option in the .mdp file, but then >> you also have to make sure you're using the appropriate >> energygrp_excl, etc. It is generally much easier to apply position >> restraints. >> >> -Justin >> >> >> Regards, >> >> Anirban >> >> >> -- ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080 >> >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- gmx-users mailing list gmx-users@gromacs.org >> <mailto:gmx-users@gromacs.org> >> >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> Please search the archive at http://www.gromacs.org/search before >> posting! >> Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org >> <mailto:gmx-users-requ...@gromacs.org>. >> >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> >> >> > -- > ======================================== > > Justin A. Lemkul > Ph.D. Candidate > ICTAS Doctoral Scholar > MILES-IGERT Trainee > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin > > ======================================== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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